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nextflow_schema.json
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nextflow_schema.json
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{
"$schema": "http://json-schema.org/draft-07/schema",
"$id": "https://raw.githubusercontent.com/nf-core/fetchngs/master/nextflow_schema.json",
"title": "nf-core/fetchngs pipeline parameters",
"description": "Pipeline to fetch metadata and raw FastQ files from public databases",
"type": "object",
"definitions": {
"input_output_options": {
"title": "Input/output options",
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Define where the pipeline should find input data and save output data.",
"required": ["input", "outdir"],
"properties": {
"input": {
"type": "string",
"format": "file-path",
"exists": true,
"schema": "assets/schema_input.json",
"mimetype": "text/csv",
"pattern": "^\\S+\\.(csv|tsv|txt)$",
"fa_icon": "fas fa-file-excel",
"description": "File containing SRA/ENA/GEO/DDBJ identifiers one per line to download their associated metadata and FastQ files."
},
"ena_metadata_fields": {
"type": "string",
"fa_icon": "fas fa-columns",
"description": "Comma-separated list of ENA metadata fields to fetch before downloading data.",
"help_text": "The default list of fields used by the pipeline can be found at the top of the [`bin/sra_ids_to_runinfo.py`](https://github.com/nf-core/fetchngs/blob/master/bin/sra_ids_to_runinfo.py) script within the pipeline repo. This pipeline requires a minimal set of fields to download FastQ files i.e. `'run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5'`. Full list of accepted metadata fields can be obtained from the [ENA API](https://www.ebi.ac.uk/ena/portal/api/returnFields?dataPortal=ena&format=tsv&result=read_run)."
},
"sample_mapping_fields": {
"type": "string",
"fa_icon": "fas fa-columns",
"description": "Comma-separated list of ENA metadata fields used to create a separate 'id_mappings.csv' and 'multiqc_config.yml' with selected fields that can be used to rename samples in general and in MultiQC.",
"default": "experiment_accession,run_accession,sample_accession,experiment_alias,run_alias,sample_alias,experiment_title,sample_title,sample_description"
},
"nf_core_pipeline": {
"type": "string",
"fa_icon": "fab fa-apple",
"description": "Name of supported nf-core pipeline e.g. 'rnaseq'. A samplesheet for direct use with the pipeline will be created with the appropriate columns.",
"enum": ["rnaseq", "atacseq", "viralrecon", "taxprofiler"]
},
"nf_core_rnaseq_strandedness": {
"type": "string",
"fa_icon": "fas fa-dna",
"description": "Value for 'strandedness' entry added to samplesheet created when using '--nf_core_pipeline rnaseq'.",
"help_text": "The default is 'auto' which can be used with nf-core/rnaseq v3.10 onwards to auto-detect strandedness during the pipeline execution.",
"default": "auto"
},
"download_method": {
"type": "string",
"default": "ftp",
"fa_icon": "fas fa-download",
"enum": ["aspera", "ftp", "sratools"],
"description": "Method to download FastQ files. Available options are 'aspera', 'ftp' or 'sratools'. Default is 'ftp'.",
"help_text": "FTP and Aspera CLI download FastQ files directly from the ENA FTP whereas sratools uses sra-tools to download *.sra files and convert to FastQ."
},
"skip_fastq_download": {
"type": "boolean",
"fa_icon": "fas fa-fast-forward",
"description": "Only download metadata for public data database ids and don't download the FastQ files."
},
"dbgap_key": {
"type": "string",
"fa_icon": "fas fa-address-card",
"help_text": "Path to a JWT cart file used to access protected dbGAP data on SRA using the sra-toolkit. Users with granted access to controlled data can download the JWT cart file for the study from the SRA Run Selector upon logging in. The JWT file can only be used on cloud platforms and is valid for 1 hour upon creation.",
"format": "file-path",
"description": "dbGaP repository key."
},
"outdir": {
"type": "string",
"format": "directory-path",
"description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
"fa_icon": "fas fa-folder-open"
},
"email": {
"type": "string",
"description": "Email address for completion summary.",
"fa_icon": "fas fa-envelope",
"help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
"pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
}
}
},
"institutional_config_options": {
"title": "Institutional config options",
"type": "object",
"fa_icon": "fas fa-university",
"description": "Parameters used to describe centralised config profiles. These should not be edited.",
"help_text": "The centralised nf-core configuration profiles use a handful of pipeline parameters to describe themselves. This information is then printed to the Nextflow log when you run a pipeline. You should not need to change these values when you run a pipeline.",
"properties": {
"custom_config_version": {
"type": "string",
"description": "Git commit id for Institutional configs.",
"default": "master",
"hidden": true,
"fa_icon": "fas fa-users-cog"
},
"custom_config_base": {
"type": "string",
"description": "Base directory for Institutional configs.",
"default": "https://raw.githubusercontent.com/nf-core/configs/master",
"hidden": true,
"help_text": "If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.",
"fa_icon": "fas fa-users-cog"
},
"config_profile_name": {
"type": "string",
"description": "Institutional config name.",
"hidden": true,
"fa_icon": "fas fa-users-cog"
},
"config_profile_description": {
"type": "string",
"description": "Institutional config description.",
"hidden": true,
"fa_icon": "fas fa-users-cog"
},
"config_profile_contact": {
"type": "string",
"description": "Institutional config contact information.",
"hidden": true,
"fa_icon": "fas fa-users-cog"
},
"config_profile_url": {
"type": "string",
"description": "Institutional config URL link.",
"hidden": true,
"fa_icon": "fas fa-users-cog"
}
}
},
"max_job_request_options": {
"title": "Max job request options",
"type": "object",
"fa_icon": "fab fa-acquisitions-incorporated",
"description": "Set the top limit for requested resources for any single job.",
"help_text": "If you are running on a smaller system, a pipeline step requesting more resources than are available may cause the Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system.\n\nNote that you can not _increase_ the resources requested by any job using these options. For that you will need your own configuration file. See [the nf-core website](https://nf-co.re/usage/configuration) for details.",
"properties": {
"max_cpus": {
"type": "integer",
"description": "Maximum number of CPUs that can be requested for any single job.",
"default": 16,
"fa_icon": "fas fa-microchip",
"hidden": true,
"help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`"
},
"max_memory": {
"type": "string",
"description": "Maximum amount of memory that can be requested for any single job.",
"default": "128.GB",
"fa_icon": "fas fa-memory",
"pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
"hidden": true,
"help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`"
},
"max_time": {
"type": "string",
"description": "Maximum amount of time that can be requested for any single job.",
"default": "240.h",
"fa_icon": "far fa-clock",
"pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$",
"hidden": true,
"help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`"
}
}
},
"generic_options": {
"title": "Generic options",
"type": "object",
"fa_icon": "fas fa-file-import",
"description": "Less common options for the pipeline, typically set in a config file.",
"help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
"properties": {
"help": {
"type": "boolean",
"description": "Display help text.",
"fa_icon": "fas fa-question-circle",
"hidden": true
},
"version": {
"type": "boolean",
"description": "Display version and exit.",
"fa_icon": "fas fa-question-circle",
"hidden": true
},
"publish_dir_mode": {
"type": "string",
"default": "copy",
"description": "Method used to save pipeline results to output directory.",
"help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
"fa_icon": "fas fa-copy",
"enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
"hidden": true
},
"email_on_fail": {
"type": "string",
"description": "Email address for completion summary, only when pipeline fails.",
"fa_icon": "fas fa-exclamation-triangle",
"pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$",
"help_text": "An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.",
"hidden": true
},
"plaintext_email": {
"type": "boolean",
"description": "Send plain-text email instead of HTML.",
"fa_icon": "fas fa-remove-format",
"hidden": true
},
"monochrome_logs": {
"type": "boolean",
"description": "Do not use coloured log outputs.",
"fa_icon": "fas fa-palette",
"hidden": true
},
"hook_url": {
"type": "string",
"description": "Incoming hook URL for messaging service",
"fa_icon": "fas fa-people-group",
"help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.",
"hidden": true
},
"validate_params": {
"type": "boolean",
"description": "Boolean whether to validate parameters against the schema at runtime",
"default": true,
"fa_icon": "fas fa-check-square",
"hidden": true
},
"validationShowHiddenParams": {
"type": "boolean",
"fa_icon": "far fa-eye-slash",
"description": "Show all params when using `--help`",
"hidden": true,
"help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
},
"validationFailUnrecognisedParams": {
"type": "boolean",
"fa_icon": "far fa-check-circle",
"description": "Validation of parameters fails when an unrecognised parameter is found.",
"hidden": true,
"help_text": "By default, when an unrecognised parameter is found, it returns a warinig."
},
"validationLenientMode": {
"type": "boolean",
"fa_icon": "far fa-check-circle",
"description": "Validation of parameters in lenient more.",
"hidden": true,
"help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)."
}
}
},
"deprecated_options": {
"title": "Deprecated options",
"type": "object",
"description": "List of parameters that have been deprecated.",
"default": "",
"fa_icon": "fas fa-calendar-times",
"properties": {
"force_sratools_download": {
"type": "boolean",
"fa_icon": "fas fa-times-circle",
"description": "This parameter has been deprecated. Please use '--download_method sratools' instead.",
"enum": [false],
"hidden": true
}
}
}
},
"allOf": [
{
"$ref": "#/definitions/input_output_options"
},
{
"$ref": "#/definitions/institutional_config_options"
},
{
"$ref": "#/definitions/max_job_request_options"
},
{
"$ref": "#/definitions/generic_options"
},
{
"$ref": "#/definitions/deprecated_options"
}
]
}